public class Modification extends ExperimentObject
Constructor and Description |
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Modification()
Constructor for the modification.
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Modification(ModificationType modificationType,
String name,
Double mass,
ArrayList<String> residues)
Simple constructor for a PTM.
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Modification(ModificationType modificationType,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification.
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Modification(ModificationType modificationType,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
CvTerm cvTerm)
Constructor for a reference modification.
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Modifier and Type | Method and Description |
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void |
addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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void |
addReporterIon(ReporterIon reporterIon)
Adds a reporter ion.
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String |
getAmbiguityKey()
Returns the ambiguity key.
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AtomChain |
getAtomChainAdded()
Returns the atom chain added.
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AtomChain |
getAtomChainRemoved()
Returns the atom chain removed.
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CvTerm |
getCvTerm()
Returns the CV term associated with this PTM.
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String |
getHtmlTooltip()
Returns information about the PTM as an HTML tooltip.
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double |
getMass()
Getter for the mass difference induced by this modification.
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ModificationType |
getModificationType()
Returns the modification type.
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String |
getName()
Getter for the modification name.
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ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the neutral losses possibly encountered with this modification.
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AminoAcidPattern |
getPattern()
Returns the amino acid pattern targeted by this modification.
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ArrayList<ReporterIon> |
getReporterIons()
Returns the reporter ions possibly encountered with this modification.
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double |
getRoundedMass()
Getter for the rounded mass difference induced by this modification.
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double |
getRoundedMass(int numberOfDecimals)
Getter for the rounded mass difference induced by this modification.
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String |
getShortName()
Getter for the short modification name.
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boolean |
isSameAs(Modification anotherPTM)
Returns true if the PTM is the same as another one.
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boolean |
isSameAtomicComposition(Modification anotherPTM)
Returns true if the atomic composition of the PTM is the same as another
one.
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boolean |
isSamePattern(Modification anotherPTM)
Returns true if the targeted pattern of the PTM is the same as another
one.
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boolean |
isStandardSearch()
Indicates whether a modification can be searched with standard search
engines, i.e., true if it targets a single amino acid position, false if
it targets a complex pattern.
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void |
setAtomChainAdded(AtomChain atomChainAdded)
Sets the atom chain added.
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void |
setAtomChainRemoved(AtomChain atomChainRemoved)
Sets the atom chain removed.
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void |
setCvTerm(CvTerm cvTerm)
Set the CV term associated with this PTM.
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void |
setName(String name)
Sets the PTM name.
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void |
setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
Sets the neutral losses possibly encountered with this modification.
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void |
setPattern(AminoAcidPattern pattern)
Sets the amino acid pattern targeted by this modification.
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void |
setReporterIons(ArrayList<ReporterIon> reporterIons)
Sets the reporter ions possibly encountered with this modification.
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void |
setShortName(String shortName)
Sets the short PTM name.
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String |
toString() |
addUrParam, asLong, clearParametersMap, getUrParam, getUrParams, removeUrParam, setUrParams
getFirstLevel, getId, setFirstLevel, setId
jdoZooEvict, jdoZooGetBackup, jdoZooGetClassDef, jdoZooGetContext, jdoZooGetNode, jdoZooGetOid, jdoZooGetTimestamp, jdoZooHasState, jdoZooInit, jdoZooIsDeleted, jdoZooIsDetached, jdoZooIsDirty, jdoZooIsNew, jdoZooIsPersistent, jdoZooIsStateHollow, jdoZooIsTransactional, jdoZooMarkClean, jdoZooMarkDeleted, jdoZooMarkDetached, jdoZooMarkDirty, jdoZooMarkHollow, jdoZooMarkTransient, jdoZooSetOid, jdoZooSetTimestamp, zooActivateRead, zooActivateWrite, zooActivateWrite
public Modification()
public Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern)
modificationType
- type of modificationname
- name of the modificationshortName
- short name of the modificationatomChainAdded
- atomic composition of the molecule addedatomChainRemoved
- atomic composition of the molecule removedaminoAcidPattern
- residue pattern affected by this modificationpublic Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, CvTerm cvTerm)
modificationType
- type of modificationname
- name of the modificationshortName
- short name of the modificationatomChainAdded
- atomic composition of the molecule addedatomChainRemoved
- atomic composition of the molecule removedaminoAcidPattern
- residue pattern affected by this modificationcvTerm
- the CV term associated with this PTM, null if not setpublic Modification(ModificationType modificationType, String name, Double mass, ArrayList<String> residues)
modificationType
- type of modificationname
- name of the modificationmass
- the mass of the modificationresidues
- list of residues possibly targeted by this modificationpublic ModificationType getModificationType()
public String getName()
public void setName(String name)
name
- the PTM namepublic String getShortName()
public void setShortName(String shortName)
shortName
- the PTM namepublic double getMass()
public String getAmbiguityKey()
public double getRoundedMass(int numberOfDecimals)
numberOfDecimals
- the number of decimals to round topublic double getRoundedMass()
public AtomChain getAtomChainAdded()
public void setAtomChainAdded(AtomChain atomChainAdded)
atomChainAdded
- the atom chain addedpublic AtomChain getAtomChainRemoved()
public void setAtomChainRemoved(AtomChain atomChainRemoved)
atomChainRemoved
- the atom chain removedpublic boolean isSameAtomicComposition(Modification anotherPTM)
anotherPTM
- the PTM to compare topublic boolean isSamePattern(Modification anotherPTM)
anotherPTM
- the PTM to compare topublic boolean isSameAs(Modification anotherPTM)
anotherPTM
- another PTMpublic ArrayList<NeutralLoss> getNeutralLosses()
public void setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- the neutral losses possibly encountered with this
modificationpublic void addNeutralLoss(NeutralLoss neutralLoss)
neutralLoss
- the new neutral losspublic ArrayList<ReporterIon> getReporterIons()
public void setReporterIons(ArrayList<ReporterIon> reporterIons)
reporterIons
- the reporter ions possibly encountered with this
modificationpublic void addReporterIon(ReporterIon reporterIon)
reporterIon
- the reporter ion to addpublic AminoAcidPattern getPattern()
public void setPattern(AminoAcidPattern pattern)
pattern
- the amino acid pattern targeted by this modificationpublic boolean isStandardSearch()
public String getHtmlTooltip()
public CvTerm getCvTerm()
public void setCvTerm(CvTerm cvTerm)
cvTerm
- the cvTerm to setpublic String toString()
toString
in class org.zoodb.api.impl.ZooPC
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